Multiple sequence alignment - TraesCS2D01G078400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G078400 chr2D 100.000 3898 0 0 1 3898 33716999 33713102 0.000000e+00 7199.0
1 TraesCS2D01G078400 chr2D 86.746 2256 274 11 3 2236 356582431 356584683 0.000000e+00 2486.0
2 TraesCS2D01G078400 chr2D 87.450 2008 225 12 25 2014 356547146 356549144 0.000000e+00 2287.0
3 TraesCS2D01G078400 chr2D 85.537 1694 177 27 2228 3898 356585564 356587212 0.000000e+00 1709.0
4 TraesCS2D01G078400 chr2A 83.649 2373 274 36 1582 3898 477082790 477085104 0.000000e+00 2128.0
5 TraesCS2D01G078400 chr2A 85.370 663 53 12 1211 1860 36535700 36535069 0.000000e+00 647.0
6 TraesCS2D01G078400 chr2A 87.273 495 58 5 342 833 36543649 36543157 9.460000e-156 560.0
7 TraesCS2D01G078400 chr2A 87.778 360 38 5 828 1184 36536051 36535695 2.170000e-112 416.0
8 TraesCS2D01G078400 chr2A 93.525 278 18 0 3 280 36626601 36626324 7.790000e-112 414.0
9 TraesCS2D01G078400 chr2A 74.603 441 75 27 3312 3732 596369981 596370404 4.030000e-35 159.0
10 TraesCS2D01G078400 chr2B 92.208 308 24 0 3 310 55873981 55873674 1.660000e-118 436.0
11 TraesCS2D01G078400 chr5D 77.431 288 49 11 3312 3590 484150023 484149743 1.450000e-34 158.0
12 TraesCS2D01G078400 chr7D 76.389 288 52 11 3312 3590 203028768 203028488 1.460000e-29 141.0
13 TraesCS2D01G078400 chr6D 72.727 286 72 6 3309 3590 102265989 102266272 1.490000e-14 91.6
14 TraesCS2D01G078400 chr7B 70.796 452 108 21 3311 3749 91197029 91197469 8.980000e-12 82.4
15 TraesCS2D01G078400 chr7B 96.875 32 1 0 3311 3342 91173932 91173963 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G078400 chr2D 33713102 33716999 3897 True 7199.0 7199 100.0000 1 3898 1 chr2D.!!$R1 3897
1 TraesCS2D01G078400 chr2D 356547146 356549144 1998 False 2287.0 2287 87.4500 25 2014 1 chr2D.!!$F1 1989
2 TraesCS2D01G078400 chr2D 356582431 356587212 4781 False 2097.5 2486 86.1415 3 3898 2 chr2D.!!$F2 3895
3 TraesCS2D01G078400 chr2A 477082790 477085104 2314 False 2128.0 2128 83.6490 1582 3898 1 chr2A.!!$F1 2316
4 TraesCS2D01G078400 chr2A 36535069 36536051 982 True 531.5 647 86.5740 828 1860 2 chr2A.!!$R3 1032

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
749 751 0.037326 TTAACAGCGAGGCAGTCCAG 60.037 55.0 0.00 0.0 33.74 3.86 F
1000 1002 0.689055 AAGCAGCAGTGGACAGATCA 59.311 50.0 0.00 0.0 0.00 2.92 F
2141 2169 0.808125 CTGAGACTGAGACCTCACCG 59.192 60.0 5.51 0.0 35.73 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1768 0.178953 AGCCTCAACATTGCCCTTGT 60.179 50.0 0.00 0.0 0.00 3.16 R
2261 3178 0.178981 CCACCCCTTCATATGGGCAG 60.179 60.0 2.13 0.0 46.43 4.85 R
3191 4149 0.172578 TCGACACCTACCAAGATGCG 59.827 55.0 0.00 0.0 0.00 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.891168 ACCCTCAAATCGGTAACAAGTTTT 59.109 37.500 0.00 0.00 0.00 2.43
77 78 2.045524 TGGGAATGAGAGATCAGAGGC 58.954 52.381 0.00 0.00 0.00 4.70
84 85 2.836372 TGAGAGATCAGAGGCACAATGT 59.164 45.455 0.00 0.00 0.00 2.71
90 91 0.386352 CAGAGGCACAATGTTGCACG 60.386 55.000 9.30 0.00 44.94 5.34
91 92 0.534877 AGAGGCACAATGTTGCACGA 60.535 50.000 9.30 0.00 44.94 4.35
139 140 0.038166 ACAGTGGCCCGTGATTGATT 59.962 50.000 0.00 0.00 0.00 2.57
142 143 0.173255 GTGGCCCGTGATTGATTTGG 59.827 55.000 0.00 0.00 0.00 3.28
152 153 4.142534 CGTGATTGATTTGGAATCAGTGCT 60.143 41.667 3.80 0.00 39.83 4.40
160 161 4.789012 TTGGAATCAGTGCTGGAAAATC 57.211 40.909 0.00 0.00 0.00 2.17
165 166 3.507162 TCAGTGCTGGAAAATCTGGAA 57.493 42.857 0.00 0.00 0.00 3.53
169 170 5.305128 TCAGTGCTGGAAAATCTGGAATTTT 59.695 36.000 0.00 0.00 34.30 1.82
183 184 2.566724 GGAATTTTGTGAAGGATGGCCA 59.433 45.455 8.56 8.56 36.29 5.36
203 204 1.888512 ACATCTGGCGCTTGAAATTGT 59.111 42.857 7.64 4.85 0.00 2.71
209 210 2.200899 GGCGCTTGAAATTGTGTTTGT 58.799 42.857 7.64 0.00 0.00 2.83
212 213 2.602211 CGCTTGAAATTGTGTTTGTGCA 59.398 40.909 0.00 0.00 0.00 4.57
218 219 3.773860 AATTGTGTTTGTGCACTCGAA 57.226 38.095 19.41 7.55 39.89 3.71
219 220 2.535934 TTGTGTTTGTGCACTCGAAC 57.464 45.000 19.41 18.67 39.89 3.95
237 238 1.145156 CCGGACCAGTGAACACACA 59.855 57.895 0.00 0.00 37.04 3.72
243 244 4.385825 GGACCAGTGAACACACAAATCTA 58.614 43.478 7.68 0.00 37.04 1.98
282 283 1.270518 GCATATCATCTGGGTCACGCT 60.271 52.381 0.00 0.00 0.00 5.07
299 300 1.756950 CTTGCTGCCATGGCCTCAT 60.757 57.895 33.44 0.00 41.09 2.90
303 304 3.804638 CTGCCATGGCCTCATCCCC 62.805 68.421 33.44 3.62 41.09 4.81
304 305 4.610526 GCCATGGCCTCATCCCCC 62.611 72.222 27.24 0.00 34.56 5.40
323 324 2.357154 CCCGATCTGGTGGAGGAAAATT 60.357 50.000 0.00 0.00 35.15 1.82
324 325 2.684881 CCGATCTGGTGGAGGAAAATTG 59.315 50.000 0.00 0.00 0.00 2.32
338 339 3.691609 GGAAAATTGAATCAGGCGAGAGT 59.308 43.478 0.00 0.00 0.00 3.24
347 348 0.179124 CAGGCGAGAGTAGAGGTTGC 60.179 60.000 0.00 0.00 0.00 4.17
350 351 0.528470 GCGAGAGTAGAGGTTGCTGT 59.472 55.000 0.00 0.00 0.00 4.40
396 397 3.937706 CGAGATTTGAGAATTCCAGCTGT 59.062 43.478 13.81 0.00 0.00 4.40
397 398 4.201792 CGAGATTTGAGAATTCCAGCTGTG 60.202 45.833 13.81 4.33 0.00 3.66
398 399 4.015084 AGATTTGAGAATTCCAGCTGTGG 58.985 43.478 13.81 0.00 46.63 4.17
413 414 4.574013 CAGCTGTGGGAAGAGACAATTATC 59.426 45.833 5.25 0.00 0.00 1.75
426 427 5.564550 AGACAATTATCAGAAGCTGGTGTT 58.435 37.500 0.00 0.00 31.51 3.32
475 476 2.550830 AACTCCGAGTTCAGTTGCAT 57.449 45.000 8.03 0.00 31.77 3.96
489 490 2.308570 AGTTGCATGGGAGGAACATGTA 59.691 45.455 0.00 0.15 45.68 2.29
491 492 2.934887 TGCATGGGAGGAACATGTATG 58.065 47.619 0.00 0.00 45.68 2.39
514 515 1.895707 GGAGATGATTGCCTGGGCG 60.896 63.158 7.14 0.00 45.51 6.13
534 535 1.401931 GCGTTCACTGCTGCAATCAAT 60.402 47.619 3.02 0.00 0.00 2.57
545 546 6.153340 ACTGCTGCAATCAATACACCTATTTT 59.847 34.615 3.02 0.00 0.00 1.82
553 554 8.491152 CAATCAATACACCTATTTTAGAGAGCG 58.509 37.037 0.00 0.00 0.00 5.03
556 557 2.165845 ACACCTATTTTAGAGAGCGCGT 59.834 45.455 8.43 0.00 0.00 6.01
558 559 4.142315 ACACCTATTTTAGAGAGCGCGTTA 60.142 41.667 8.43 0.00 0.00 3.18
568 569 0.179119 GAGCGCGTTAGAAGGCCTTA 60.179 55.000 20.54 0.00 36.51 2.69
617 618 0.465824 ATGAGATGCTTGCCTCCTGC 60.466 55.000 0.00 0.00 41.77 4.85
643 644 1.287191 GGATCTAGCTCATGCGCGA 59.713 57.895 12.10 0.00 45.42 5.87
676 677 3.680620 ATGGGCGACATCGGTGGTG 62.681 63.158 0.00 0.00 40.23 4.17
680 681 2.094659 GCGACATCGGTGGTGTCAG 61.095 63.158 10.50 4.79 44.77 3.51
685 686 1.416401 ACATCGGTGGTGTCAGTTTCT 59.584 47.619 0.00 0.00 0.00 2.52
702 704 3.297134 TTCTTTCAGAGTTGCAAGGGT 57.703 42.857 0.00 0.00 29.87 4.34
725 727 4.164294 GCTAGAGTTCGAGCGTAGAAAAA 58.836 43.478 13.42 0.00 35.06 1.94
736 738 6.089016 TCGAGCGTAGAAAAATCAGTTAACAG 59.911 38.462 8.61 0.00 0.00 3.16
749 751 0.037326 TTAACAGCGAGGCAGTCCAG 60.037 55.000 0.00 0.00 33.74 3.86
754 756 2.997315 CGAGGCAGTCCAGGTGGA 60.997 66.667 0.00 0.00 43.08 4.02
767 769 1.153823 GGTGGACGATGAGGTCACG 60.154 63.158 0.00 0.00 38.70 4.35
785 787 2.203153 ACGCACTTCGCCCAACTT 60.203 55.556 0.00 0.00 43.23 2.66
798 800 3.248043 CAACTTTGGAGCCCATCGA 57.752 52.632 0.00 0.00 31.53 3.59
803 805 2.178876 TTTGGAGCCCATCGAAGCGA 62.179 55.000 0.00 0.00 41.13 4.93
825 827 2.767394 TGTGCGGATAAAGCTAGGGTTA 59.233 45.455 0.00 0.00 35.28 2.85
904 906 2.632377 CGCCACCACTGTAGATTCAAT 58.368 47.619 0.00 0.00 0.00 2.57
909 911 3.804325 CACCACTGTAGATTCAATAGCCG 59.196 47.826 0.00 0.00 0.00 5.52
946 948 1.208293 GAGAGGCCGAGGAAAGAACAT 59.792 52.381 0.00 0.00 0.00 2.71
974 976 1.073763 CAGGGAGATGGTGACCAACAA 59.926 52.381 9.06 0.00 36.95 2.83
994 996 2.464157 AACTAGAAGCAGCAGTGGAC 57.536 50.000 0.00 0.00 0.00 4.02
1000 1002 0.689055 AAGCAGCAGTGGACAGATCA 59.311 50.000 0.00 0.00 0.00 2.92
1048 1051 1.488393 CCCCTTTGCTTTTGGGTTTGA 59.512 47.619 0.00 0.00 39.31 2.69
1072 1075 4.035102 GGGACAGCCACCACCCTC 62.035 72.222 0.00 0.00 39.28 4.30
1083 1086 1.303236 CCACCCTCGGCATTCAACA 60.303 57.895 0.00 0.00 0.00 3.33
1230 1236 2.438021 AGCAACACTGGTCAAGGTTCTA 59.562 45.455 0.00 0.00 0.00 2.10
1235 1241 4.737578 ACACTGGTCAAGGTTCTAGTAGA 58.262 43.478 0.00 0.00 0.00 2.59
1250 1256 5.875224 TCTAGTAGATCTGGGATCTCTGTG 58.125 45.833 12.53 8.36 0.00 3.66
1252 1258 1.422531 AGATCTGGGATCTCTGTGCC 58.577 55.000 0.00 0.00 0.00 5.01
1374 1380 0.916086 TTGTGGTGGTTGTGGAGAGT 59.084 50.000 0.00 0.00 0.00 3.24
1486 1492 6.098552 AGGAAGAAACCTAATCTAGCTACCAC 59.901 42.308 0.00 0.00 38.65 4.16
1541 1547 5.791336 TCTACCATGTGGATATGTCAGAC 57.209 43.478 5.96 0.00 38.94 3.51
1560 1566 4.680110 CAGACGTTAACCTACAACACTCTG 59.320 45.833 0.00 0.00 30.27 3.35
1589 1595 7.177392 AGACTTAAGAATGGAGGGATTGTTTTG 59.823 37.037 10.09 0.00 0.00 2.44
1590 1596 6.211384 ACTTAAGAATGGAGGGATTGTTTTGG 59.789 38.462 10.09 0.00 0.00 3.28
1596 1602 5.269554 TGGAGGGATTGTTTTGGTAGAAT 57.730 39.130 0.00 0.00 0.00 2.40
1597 1603 5.650283 TGGAGGGATTGTTTTGGTAGAATT 58.350 37.500 0.00 0.00 0.00 2.17
1614 1620 4.419282 AGAATTTGGGGAGATCAGCAAAA 58.581 39.130 0.00 0.00 0.00 2.44
1623 1629 4.385754 GGGAGATCAGCAAAAAGGACCTAT 60.386 45.833 0.00 0.00 0.00 2.57
1708 1714 5.018539 TGGACCATATTAGTGAAGTTCCG 57.981 43.478 0.00 0.00 0.00 4.30
1753 1762 1.133637 TGCCAGTTACCCTTGCTTTGA 60.134 47.619 0.00 0.00 33.08 2.69
1757 1766 3.222603 CAGTTACCCTTGCTTTGACCTT 58.777 45.455 0.00 0.00 0.00 3.50
1759 1768 3.117663 AGTTACCCTTGCTTTGACCTTCA 60.118 43.478 0.00 0.00 0.00 3.02
1790 1811 2.158325 TGTTGAGGCTTGGAAAGGGAAT 60.158 45.455 0.00 0.00 46.35 3.01
1796 1817 4.281657 AGGCTTGGAAAGGGAATATTGAC 58.718 43.478 0.00 0.00 46.35 3.18
1798 1819 3.945285 GCTTGGAAAGGGAATATTGACGA 59.055 43.478 0.00 0.00 46.35 4.20
1803 1824 5.659525 TGGAAAGGGAATATTGACGACTCTA 59.340 40.000 0.00 0.00 0.00 2.43
1805 1826 4.832590 AGGGAATATTGACGACTCTACG 57.167 45.455 0.00 0.00 39.31 3.51
1871 1893 6.319048 AGATGGTGTGAATGGTCTATTCTT 57.681 37.500 9.98 0.00 44.49 2.52
1894 1916 6.633500 TGACCAAATTACTTCTGTCTTTGG 57.367 37.500 10.05 10.05 45.18 3.28
1899 1921 3.569194 TTACTTCTGTCTTTGGCACCA 57.431 42.857 0.00 0.00 0.00 4.17
1909 1931 1.406539 CTTTGGCACCATAGTGGATGC 59.593 52.381 2.45 8.62 44.69 3.91
1917 1939 1.072173 CCATAGTGGATGCGGATTGGA 59.928 52.381 0.00 0.00 40.96 3.53
1925 1947 3.119173 TGGATGCGGATTGGAAATTCAAC 60.119 43.478 0.00 0.00 0.00 3.18
1933 1959 6.147656 GCGGATTGGAAATTCAACTTCAAAAT 59.852 34.615 0.00 0.00 0.00 1.82
1946 1972 8.924511 TCAACTTCAAAATCTTCTATGAGGTT 57.075 30.769 0.00 0.00 41.11 3.50
1950 1976 7.175641 ACTTCAAAATCTTCTATGAGGTTGTGG 59.824 37.037 0.00 0.00 29.06 4.17
1951 1977 5.945784 TCAAAATCTTCTATGAGGTTGTGGG 59.054 40.000 0.00 0.00 27.99 4.61
1975 2001 6.371825 GGAGTTAAGTTGTCCTGTAAAGATGG 59.628 42.308 0.00 0.00 0.00 3.51
2016 2042 9.804977 AGGAAAGAATCTATGGAATAAATGGAG 57.195 33.333 0.00 0.00 0.00 3.86
2038 2065 6.969473 GGAGAGTTCTACAAAATGCTTATTGC 59.031 38.462 0.00 0.00 43.25 3.56
2039 2066 6.546395 AGAGTTCTACAAAATGCTTATTGCG 58.454 36.000 0.00 0.00 46.63 4.85
2047 2074 1.832883 ATGCTTATTGCGGTGGAACA 58.167 45.000 0.00 0.00 46.63 3.18
2096 2124 8.055181 ACTGGGACTGATAACAATGATACAATT 58.945 33.333 0.00 0.00 0.00 2.32
2098 2126 9.559732 TGGGACTGATAACAATGATACAATTAG 57.440 33.333 0.00 0.00 0.00 1.73
2139 2167 3.509575 ACAATCTGAGACTGAGACCTCAC 59.490 47.826 0.00 0.00 35.73 3.51
2141 2169 0.808125 CTGAGACTGAGACCTCACCG 59.192 60.000 5.51 0.00 35.73 4.94
2204 2232 3.400054 GGGAGAGGGGGTGGTTCG 61.400 72.222 0.00 0.00 0.00 3.95
2229 2257 3.005791 CCCTACTTTGGAAAAACAGGCAG 59.994 47.826 0.00 0.00 0.00 4.85
2269 3186 1.216064 ATGCCAGAAGTCTGCCCATA 58.784 50.000 2.59 0.00 42.47 2.74
2300 3217 5.698741 TGGAACATCCATCACTACTCAAT 57.301 39.130 0.00 0.00 42.67 2.57
2302 3219 7.379059 TGGAACATCCATCACTACTCAATAT 57.621 36.000 0.00 0.00 42.67 1.28
2307 3224 8.255111 ACATCCATCACTACTCAATATTCAGA 57.745 34.615 0.00 0.00 0.00 3.27
2310 3239 8.718158 TCCATCACTACTCAATATTCAGATCT 57.282 34.615 0.00 0.00 0.00 2.75
2315 3244 8.001292 TCACTACTCAATATTCAGATCTCTCCA 58.999 37.037 0.00 0.00 0.00 3.86
2319 3248 6.786461 ACTCAATATTCAGATCTCTCCATCCA 59.214 38.462 0.00 0.00 0.00 3.41
2339 3268 0.692419 TCCAGGCCTCAAGGAGATCC 60.692 60.000 0.00 0.00 37.39 3.36
2348 3277 4.446023 GCCTCAAGGAGATCCAAGATTGAT 60.446 45.833 0.00 0.00 38.89 2.57
2360 3289 6.499106 TCCAAGATTGATAAGATAGTGGCA 57.501 37.500 0.00 0.00 0.00 4.92
2365 3294 9.716531 CAAGATTGATAAGATAGTGGCAGAATA 57.283 33.333 0.00 0.00 0.00 1.75
2396 3325 5.604231 TGATGACCAATGCTACTCTATCCTT 59.396 40.000 0.00 0.00 0.00 3.36
2399 3328 6.136857 TGACCAATGCTACTCTATCCTTAGT 58.863 40.000 0.00 0.00 0.00 2.24
2409 3338 7.231722 GCTACTCTATCCTTAGTGAAATGGAGA 59.768 40.741 0.00 0.00 32.77 3.71
2417 3346 2.996631 AGTGAAATGGAGATGGCTGAC 58.003 47.619 0.00 0.00 0.00 3.51
2418 3347 2.575279 AGTGAAATGGAGATGGCTGACT 59.425 45.455 0.00 0.00 0.00 3.41
2444 3394 1.912043 CAAGAGATGGAGGAGGTTGGT 59.088 52.381 0.00 0.00 0.00 3.67
2461 3411 1.754745 GTGACACCCAGGAGCAAGA 59.245 57.895 0.00 0.00 0.00 3.02
2476 3426 3.937706 GAGCAAGATGTTGTAGCATCAGT 59.062 43.478 10.62 0.00 45.58 3.41
2516 3466 5.127845 CACTTATGAGGCTGACTTTCCTCTA 59.872 44.000 9.38 0.00 46.90 2.43
2535 3485 5.594725 CCTCTACTATCCAAGACAGTTGCTA 59.405 44.000 0.00 0.00 0.00 3.49
2559 3509 5.376625 ACAAGCAACAGAAATAGAAGTGGA 58.623 37.500 0.00 0.00 0.00 4.02
2565 3515 3.054802 ACAGAAATAGAAGTGGAGGCCAG 60.055 47.826 5.01 0.00 32.34 4.85
2597 3547 0.467290 GGCACAACTCAAGGGTGGAA 60.467 55.000 0.00 0.00 36.85 3.53
2616 3566 3.306710 GGAACCCTTTGGCAAAACTATGG 60.307 47.826 14.43 10.79 33.59 2.74
2625 3575 4.415596 TGGCAAAACTATGGTGGAGAAAT 58.584 39.130 0.00 0.00 0.00 2.17
2634 3584 6.725364 ACTATGGTGGAGAAATCACAAGAAT 58.275 36.000 0.00 0.00 36.90 2.40
2649 3599 6.808829 TCACAAGAATTCAAGCAAGTGAAAT 58.191 32.000 8.44 0.00 40.76 2.17
2659 3609 8.592105 TTCAAGCAAGTGAAATATTTGGAAAG 57.408 30.769 5.17 0.00 34.59 2.62
2661 3611 7.652909 TCAAGCAAGTGAAATATTTGGAAAGTG 59.347 33.333 5.17 0.00 0.00 3.16
2667 3617 8.729805 AGTGAAATATTTGGAAAGTGCAAAAA 57.270 26.923 5.17 0.00 40.92 1.94
2668 3618 9.341078 AGTGAAATATTTGGAAAGTGCAAAAAT 57.659 25.926 5.17 0.00 40.92 1.82
2674 3624 6.670077 TTTGGAAAGTGCAAAAATTGGTAC 57.330 33.333 0.00 0.00 34.76 3.34
2694 3644 2.627699 ACGAACCAACATGCATTTTCCT 59.372 40.909 0.00 0.00 0.00 3.36
2719 3669 8.728596 TTTTTCAATAACCCCTCCTTTATTGA 57.271 30.769 11.08 11.08 46.04 2.57
2724 3674 7.559897 TCAATAACCCCTCCTTTATTGATGTTC 59.440 37.037 11.08 0.00 44.28 3.18
2729 3682 6.064717 CCCCTCCTTTATTGATGTTCCTAAG 58.935 44.000 0.00 0.00 0.00 2.18
2764 3722 7.576861 TGGATATTGACGAACATAGTAGTCA 57.423 36.000 0.00 4.87 41.24 3.41
2766 3724 8.297426 TGGATATTGACGAACATAGTAGTCATC 58.703 37.037 8.47 5.04 42.29 2.92
2777 3735 6.300703 ACATAGTAGTCATCCTCCTAGTCAC 58.699 44.000 0.00 0.00 0.00 3.67
2814 3772 2.555227 CCAATTGACACCCTAGCTGGTT 60.555 50.000 7.12 0.00 36.12 3.67
2822 3780 5.190925 TGACACCCTAGCTGGTTAATGTAAT 59.809 40.000 0.00 0.00 36.12 1.89
2827 3785 6.614087 ACCCTAGCTGGTTAATGTAATGTAGA 59.386 38.462 0.00 0.00 33.91 2.59
2831 3789 7.849804 AGCTGGTTAATGTAATGTAGAACTG 57.150 36.000 0.00 0.00 0.00 3.16
2931 3889 5.584253 TTCTCCTACTAGCATTGAGACAC 57.416 43.478 0.00 0.00 32.16 3.67
2953 3911 3.260884 CGGGTTGTGGCCTATGACTATAT 59.739 47.826 3.32 0.00 0.00 0.86
2955 3913 5.623824 CGGGTTGTGGCCTATGACTATATAC 60.624 48.000 3.32 0.00 0.00 1.47
2957 3915 5.408356 GTTGTGGCCTATGACTATATACGG 58.592 45.833 3.32 0.00 0.00 4.02
2997 3955 6.293626 GGCTACAGTTATACCATGAATTGCTG 60.294 42.308 0.00 2.81 0.00 4.41
2998 3956 6.483307 GCTACAGTTATACCATGAATTGCTGA 59.517 38.462 0.00 0.00 0.00 4.26
3004 3962 8.970020 AGTTATACCATGAATTGCTGATTTTGA 58.030 29.630 0.00 0.00 0.00 2.69
3019 3977 3.681593 TTTTGAAATGTGAGGGGCATG 57.318 42.857 0.00 0.00 0.00 4.06
3020 3978 0.896923 TTGAAATGTGAGGGGCATGC 59.103 50.000 9.90 9.90 0.00 4.06
3073 4031 7.716799 AGATTGCATTGGTAAGATAAAACCA 57.283 32.000 0.00 0.00 43.99 3.67
3085 4043 7.778382 GGTAAGATAAAACCATCCATTGTAGGT 59.222 37.037 0.00 0.00 35.73 3.08
3114 4072 6.249035 AGAGACTACGAAAGAGAGTTTCTG 57.751 41.667 0.00 0.00 39.05 3.02
3115 4073 4.800784 AGACTACGAAAGAGAGTTTCTGC 58.199 43.478 0.00 0.00 35.91 4.26
3125 4083 3.827302 AGAGAGTTTCTGCGACTCCTTTA 59.173 43.478 0.96 0.00 43.55 1.85
3132 4090 6.431234 AGTTTCTGCGACTCCTTTATGAAATT 59.569 34.615 0.00 0.00 0.00 1.82
3149 4107 6.877611 TGAAATTCTTGGTTAGTGGAAGAC 57.122 37.500 0.00 0.00 0.00 3.01
3191 4149 3.265791 CCAGTCATTGGTTCAGCTAGAC 58.734 50.000 0.00 0.00 42.41 2.59
3193 4151 1.661112 GTCATTGGTTCAGCTAGACGC 59.339 52.381 0.00 0.00 39.57 5.19
3197 4155 1.186200 TGGTTCAGCTAGACGCATCT 58.814 50.000 0.00 0.00 42.61 2.90
3200 4158 1.929836 GTTCAGCTAGACGCATCTTGG 59.070 52.381 0.00 0.00 42.61 3.61
3208 4166 1.204941 AGACGCATCTTGGTAGGTGTC 59.795 52.381 0.00 0.00 40.18 3.67
3222 4181 6.598503 TGGTAGGTGTCGATCTAGATCTTTA 58.401 40.000 26.29 11.92 35.72 1.85
3282 4241 9.268268 TGTCTCATGTACTGTTAGGTTAAAAAG 57.732 33.333 0.00 0.00 0.00 2.27
3311 4270 9.915629 AACAACTAGAGTTTAGAATAGTCACAG 57.084 33.333 0.00 0.00 35.83 3.66
3344 4303 4.415512 CCCCATATGAGGAGGGTAAAGAAA 59.584 45.833 3.65 0.00 41.16 2.52
3416 4377 4.415512 CCTTGGTAGGGGGATTTCAATCTA 59.584 45.833 0.00 0.00 37.94 1.98
3450 4412 9.775854 TTAACCATGATAAAATTAATGGGCATG 57.224 29.630 0.00 0.00 43.26 4.06
3541 4503 4.435137 TCCTCCAGAAAGATTACTTGGGA 58.565 43.478 0.00 0.00 36.39 4.37
3555 4517 8.778059 AGATTACTTGGGATAATAACCAGTCAA 58.222 33.333 0.00 0.00 38.16 3.18
3576 4538 9.988815 AGTCAAATAACATCATCTCTACCATAC 57.011 33.333 0.00 0.00 0.00 2.39
3628 4590 2.634453 AGTTTTTCCCTTTGGCCTCATG 59.366 45.455 3.32 0.00 0.00 3.07
3629 4591 2.368548 GTTTTTCCCTTTGGCCTCATGT 59.631 45.455 3.32 0.00 0.00 3.21
3685 4647 2.224867 CCACTGTCTGGGATTCAGGTTT 60.225 50.000 0.00 0.00 43.53 3.27
3688 4650 3.650942 ACTGTCTGGGATTCAGGTTTGTA 59.349 43.478 0.00 0.00 43.53 2.41
3695 4657 7.175990 GTCTGGGATTCAGGTTTGTATAAACAA 59.824 37.037 15.80 3.63 46.28 2.83
3732 4694 9.516314 GTAGTTATAAATTTGAGAAATGGTGGC 57.484 33.333 0.00 0.00 0.00 5.01
3733 4695 8.366359 AGTTATAAATTTGAGAAATGGTGGCT 57.634 30.769 0.00 0.00 0.00 4.75
3734 4696 8.470002 AGTTATAAATTTGAGAAATGGTGGCTC 58.530 33.333 0.00 0.00 0.00 4.70
3735 4697 4.541973 AAATTTGAGAAATGGTGGCTCC 57.458 40.909 0.00 0.00 0.00 4.70
3736 4698 2.978156 TTTGAGAAATGGTGGCTCCT 57.022 45.000 7.19 0.00 37.07 3.69
3737 4699 2.978156 TTGAGAAATGGTGGCTCCTT 57.022 45.000 7.19 0.00 37.07 3.36
3738 4700 4.380843 TTTGAGAAATGGTGGCTCCTTA 57.619 40.909 7.19 0.00 37.07 2.69
3739 4701 3.634397 TGAGAAATGGTGGCTCCTTAG 57.366 47.619 7.19 0.00 37.07 2.18
3740 4702 3.181329 TGAGAAATGGTGGCTCCTTAGA 58.819 45.455 7.19 0.00 37.07 2.10
3741 4703 3.198635 TGAGAAATGGTGGCTCCTTAGAG 59.801 47.826 7.19 0.00 43.57 2.43
3742 4704 3.452627 GAGAAATGGTGGCTCCTTAGAGA 59.547 47.826 7.19 0.00 43.39 3.10
3743 4705 3.454082 AGAAATGGTGGCTCCTTAGAGAG 59.546 47.826 7.19 0.00 43.39 3.20
3762 4724 7.569599 AGAGAGGATTTCCAAACCTTAGTTA 57.430 36.000 0.00 0.00 38.89 2.24
3773 4735 8.990163 TCCAAACCTTAGTTAAGAAGAATTGT 57.010 30.769 0.51 0.00 34.19 2.71
3845 4807 8.885693 AAATTAGAAGATTTAGGAAAGCCACT 57.114 30.769 0.00 0.00 36.29 4.00
3846 4808 9.975218 AAATTAGAAGATTTAGGAAAGCCACTA 57.025 29.630 0.00 0.00 36.29 2.74
3867 4829 6.597672 CACTATAAATGGTGGAGTAGCAACAA 59.402 38.462 0.00 0.00 40.70 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.009210 TCCCAAAACTTGTTACCGATTTGAG 59.991 40.000 0.00 0.00 31.23 3.02
38 39 4.888239 TCCCAAAACTTGTTACCGATTTGA 59.112 37.500 0.00 0.00 31.23 2.69
57 58 2.045524 GCCTCTGATCTCTCATTCCCA 58.954 52.381 0.00 0.00 0.00 4.37
90 91 4.333649 TGCATATCTACAGTTGCTTTGCTC 59.666 41.667 3.79 0.00 36.10 4.26
91 92 4.264253 TGCATATCTACAGTTGCTTTGCT 58.736 39.130 3.79 0.00 36.10 3.91
139 140 4.219070 CAGATTTTCCAGCACTGATTCCAA 59.781 41.667 0.00 0.00 0.00 3.53
142 143 4.012374 TCCAGATTTTCCAGCACTGATTC 58.988 43.478 0.00 0.00 0.00 2.52
152 153 6.326064 TCCTTCACAAAATTCCAGATTTTCCA 59.674 34.615 0.00 0.00 0.00 3.53
160 161 3.368739 GGCCATCCTTCACAAAATTCCAG 60.369 47.826 0.00 0.00 0.00 3.86
165 166 2.607499 TGTGGCCATCCTTCACAAAAT 58.393 42.857 9.72 0.00 38.30 1.82
169 170 3.575506 GATGTGGCCATCCTTCACA 57.424 52.632 9.72 0.00 44.12 3.58
183 184 1.888512 ACAATTTCAAGCGCCAGATGT 59.111 42.857 2.29 0.94 0.00 3.06
203 204 1.433053 CCGGTTCGAGTGCACAAACA 61.433 55.000 21.04 0.00 0.00 2.83
209 210 3.220999 CTGGTCCGGTTCGAGTGCA 62.221 63.158 0.00 0.00 0.00 4.57
212 213 1.111116 TTCACTGGTCCGGTTCGAGT 61.111 55.000 0.00 6.30 0.00 4.18
218 219 1.145377 GTGTGTTCACTGGTCCGGT 59.855 57.895 0.00 0.00 40.98 5.28
219 220 0.462937 TTGTGTGTTCACTGGTCCGG 60.463 55.000 0.00 0.00 44.14 5.14
237 238 3.840078 AGGCCAAACCAAGCATTAGATTT 59.160 39.130 5.01 0.00 43.14 2.17
243 244 0.971386 CAGAGGCCAAACCAAGCATT 59.029 50.000 5.01 0.00 43.14 3.56
282 283 1.755395 GATGAGGCCATGGCAGCAA 60.755 57.895 36.56 19.70 44.11 3.91
303 304 2.684881 CAATTTTCCTCCACCAGATCGG 59.315 50.000 2.55 2.55 42.50 4.18
304 305 3.609853 TCAATTTTCCTCCACCAGATCG 58.390 45.455 0.00 0.00 0.00 3.69
323 324 2.302260 CCTCTACTCTCGCCTGATTCA 58.698 52.381 0.00 0.00 0.00 2.57
324 325 2.303175 ACCTCTACTCTCGCCTGATTC 58.697 52.381 0.00 0.00 0.00 2.52
338 339 4.526650 TCTGTATTGTGACAGCAACCTCTA 59.473 41.667 0.00 0.00 45.44 2.43
347 348 6.873605 TGGAGTTGTAATCTGTATTGTGACAG 59.126 38.462 0.00 0.00 46.90 3.51
350 351 5.874810 GCTGGAGTTGTAATCTGTATTGTGA 59.125 40.000 0.00 0.00 0.00 3.58
362 363 4.021456 TCTCAAATCTCGCTGGAGTTGTAA 60.021 41.667 12.91 3.82 40.65 2.41
363 364 3.509967 TCTCAAATCTCGCTGGAGTTGTA 59.490 43.478 12.91 4.06 40.65 2.41
364 365 2.300152 TCTCAAATCTCGCTGGAGTTGT 59.700 45.455 12.91 0.00 40.65 3.32
396 397 5.190528 AGCTTCTGATAATTGTCTCTTCCCA 59.809 40.000 3.72 0.00 0.00 4.37
397 398 5.526846 CAGCTTCTGATAATTGTCTCTTCCC 59.473 44.000 3.72 0.00 32.44 3.97
398 399 5.526846 CCAGCTTCTGATAATTGTCTCTTCC 59.473 44.000 3.72 0.00 32.44 3.46
413 414 3.405831 TGATTCTCAACACCAGCTTCTG 58.594 45.455 0.00 0.00 0.00 3.02
426 427 1.756538 TGGCAGCTACGATGATTCTCA 59.243 47.619 0.00 0.00 0.00 3.27
437 438 1.153549 CCTCTTCGGTGGCAGCTAC 60.154 63.158 15.48 0.00 0.00 3.58
441 442 0.390472 GAGTTCCTCTTCGGTGGCAG 60.390 60.000 0.00 0.00 0.00 4.85
475 476 0.180171 CCGCATACATGTTCCTCCCA 59.820 55.000 2.30 0.00 0.00 4.37
489 490 0.250640 GGCAATCATCTCCTCCGCAT 60.251 55.000 0.00 0.00 0.00 4.73
491 492 0.883814 CAGGCAATCATCTCCTCCGC 60.884 60.000 0.00 0.00 0.00 5.54
514 515 0.040157 TTGATTGCAGCAGTGAACGC 60.040 50.000 0.00 0.00 0.00 4.84
524 525 9.330063 TCTCTAAAATAGGTGTATTGATTGCAG 57.670 33.333 0.00 0.00 0.00 4.41
527 528 8.491152 CGCTCTCTAAAATAGGTGTATTGATTG 58.509 37.037 0.00 0.00 0.00 2.67
534 535 3.379372 ACGCGCTCTCTAAAATAGGTGTA 59.621 43.478 5.73 0.00 0.00 2.90
545 546 0.381089 GCCTTCTAACGCGCTCTCTA 59.619 55.000 5.73 0.00 0.00 2.43
553 554 1.140252 TCCCATAAGGCCTTCTAACGC 59.860 52.381 24.49 0.00 34.51 4.84
556 557 4.480537 TGGATTTCCCATAAGGCCTTCTAA 59.519 41.667 24.49 4.75 40.82 2.10
558 559 2.858768 TGGATTTCCCATAAGGCCTTCT 59.141 45.455 24.49 10.01 40.82 2.85
568 569 1.797320 CCCAATGCTGGATTTCCCAT 58.203 50.000 0.00 0.00 46.92 4.00
617 618 2.079170 TGAGCTAGATCCCTGAGGTG 57.921 55.000 5.36 0.00 0.00 4.00
643 644 1.830279 CCCATGATCAACTGCAGTGT 58.170 50.000 22.49 9.88 0.00 3.55
676 677 4.882671 TGCAACTCTGAAAGAAACTGAC 57.117 40.909 0.00 0.00 46.34 3.51
680 681 3.381590 ACCCTTGCAACTCTGAAAGAAAC 59.618 43.478 0.00 0.00 46.34 2.78
702 704 2.019948 TCTACGCTCGAACTCTAGCA 57.980 50.000 4.37 0.00 38.70 3.49
705 707 5.946298 TGATTTTTCTACGCTCGAACTCTA 58.054 37.500 0.00 0.00 0.00 2.43
725 727 1.276421 ACTGCCTCGCTGTTAACTGAT 59.724 47.619 15.89 0.00 37.43 2.90
736 738 4.767255 CCACCTGGACTGCCTCGC 62.767 72.222 0.00 0.00 37.39 5.03
749 751 1.153823 CGTGACCTCATCGTCCACC 60.154 63.158 0.00 0.00 31.35 4.61
754 756 2.178521 GCGTCGTGACCTCATCGT 59.821 61.111 0.00 0.00 0.00 3.73
785 787 1.971505 ATCGCTTCGATGGGCTCCAA 61.972 55.000 10.13 0.00 45.24 3.53
796 798 0.927537 TTTATCCGCACATCGCTTCG 59.072 50.000 0.00 0.00 39.08 3.79
798 800 0.657840 GCTTTATCCGCACATCGCTT 59.342 50.000 0.00 0.00 39.08 4.68
803 805 1.768870 ACCCTAGCTTTATCCGCACAT 59.231 47.619 0.00 0.00 0.00 3.21
808 810 3.258622 CCTCCTAACCCTAGCTTTATCCG 59.741 52.174 0.00 0.00 0.00 4.18
825 827 2.462723 GAGGTCTTGAAGTAGCCTCCT 58.537 52.381 16.34 6.69 39.69 3.69
904 906 1.219664 CGGTTGGAATCCACGGCTA 59.780 57.895 0.00 0.00 30.78 3.93
974 976 2.104792 TGTCCACTGCTGCTTCTAGTTT 59.895 45.455 0.00 0.00 0.00 2.66
994 996 1.676746 CATCTGCAGGGGTTGATCTG 58.323 55.000 15.13 0.00 0.00 2.90
1048 1051 3.637273 GTGGCTGTCCCGGGAACT 61.637 66.667 28.84 0.00 35.87 3.01
1067 1070 0.893727 GGTTGTTGAATGCCGAGGGT 60.894 55.000 0.00 0.00 0.00 4.34
1072 1075 1.335872 GGAACTGGTTGTTGAATGCCG 60.336 52.381 0.00 0.00 39.30 5.69
1083 1086 4.367590 TCCCCCATGGAACTGGTT 57.632 55.556 15.22 0.00 41.40 3.67
1111 1117 1.599518 CCTTGCCACTGTTGCGGTA 60.600 57.895 0.00 0.00 0.00 4.02
1112 1118 2.906897 CCTTGCCACTGTTGCGGT 60.907 61.111 0.00 0.00 0.00 5.68
1118 1124 0.250901 GTGACATCCCTTGCCACTGT 60.251 55.000 0.00 0.00 35.95 3.55
1177 1183 1.004044 CTTGATCTCCACCCTGTTGCT 59.996 52.381 0.00 0.00 0.00 3.91
1230 1236 3.230134 GCACAGAGATCCCAGATCTACT 58.770 50.000 7.08 4.44 0.00 2.57
1235 1241 3.329497 TGGCACAGAGATCCCAGAT 57.671 52.632 0.00 0.00 0.00 2.90
1250 1256 4.019174 TCTGATTTTTCTGATTCCCTGGC 58.981 43.478 0.00 0.00 0.00 4.85
1252 1258 4.703575 TGCTCTGATTTTTCTGATTCCCTG 59.296 41.667 0.00 0.00 0.00 4.45
1374 1380 4.635223 CACTTCTCTTTGTCATGACCTGA 58.365 43.478 22.85 15.74 0.00 3.86
1436 1442 2.172505 TGGACAGTTGTGTTCCTGATGT 59.827 45.455 0.00 0.00 36.88 3.06
1473 1479 4.142004 CCCAAAGTACGTGGTAGCTAGATT 60.142 45.833 15.11 0.00 34.01 2.40
1482 1488 0.250166 GCACTCCCAAAGTACGTGGT 60.250 55.000 15.11 0.00 36.07 4.16
1486 1492 0.320771 AGCTGCACTCCCAAAGTACG 60.321 55.000 1.02 0.00 36.07 3.67
1509 1515 3.069586 TCCACATGGTAGAAGCCTAATCG 59.930 47.826 0.00 0.00 36.34 3.34
1541 1547 3.006110 TCCCAGAGTGTTGTAGGTTAACG 59.994 47.826 0.00 0.00 0.00 3.18
1560 1566 3.385115 TCCCTCCATTCTTAAGTCTCCC 58.615 50.000 1.63 0.00 0.00 4.30
1589 1595 3.117888 TGCTGATCTCCCCAAATTCTACC 60.118 47.826 0.00 0.00 0.00 3.18
1590 1596 4.156455 TGCTGATCTCCCCAAATTCTAC 57.844 45.455 0.00 0.00 0.00 2.59
1596 1602 2.899256 CCTTTTTGCTGATCTCCCCAAA 59.101 45.455 0.00 0.00 0.00 3.28
1597 1603 2.109834 TCCTTTTTGCTGATCTCCCCAA 59.890 45.455 0.00 0.00 0.00 4.12
1614 1620 8.380742 TCTGAGAATTTAGTTGATAGGTCCTT 57.619 34.615 0.00 0.00 0.00 3.36
1708 1714 4.526970 TGATTCTACAGGAATTTCAGGGC 58.473 43.478 0.00 0.00 43.90 5.19
1757 1766 1.619654 CCTCAACATTGCCCTTGTGA 58.380 50.000 0.00 0.00 0.00 3.58
1759 1768 0.178953 AGCCTCAACATTGCCCTTGT 60.179 50.000 0.00 0.00 0.00 3.16
1764 1773 0.968405 TTCCAAGCCTCAACATTGCC 59.032 50.000 0.00 0.00 0.00 4.52
1798 1819 4.117685 GACCAACTGTTTTGACGTAGAGT 58.882 43.478 0.00 0.00 0.00 3.24
1803 1824 2.014128 CCAGACCAACTGTTTTGACGT 58.986 47.619 0.00 0.00 44.40 4.34
1805 1826 6.385649 TTTATCCAGACCAACTGTTTTGAC 57.614 37.500 0.00 0.00 44.40 3.18
1809 1830 8.585018 CCTAATTTTTATCCAGACCAACTGTTT 58.415 33.333 0.00 0.00 44.40 2.83
1871 1893 5.009610 GCCAAAGACAGAAGTAATTTGGTCA 59.990 40.000 18.33 0.00 46.43 4.02
1894 1916 0.250467 ATCCGCATCCACTATGGTGC 60.250 55.000 3.19 10.54 41.75 5.01
1899 1921 3.576078 TTTCCAATCCGCATCCACTAT 57.424 42.857 0.00 0.00 0.00 2.12
1909 1931 7.599998 AGATTTTGAAGTTGAATTTCCAATCCG 59.400 33.333 13.83 0.00 30.72 4.18
1925 1947 7.362401 CCCACAACCTCATAGAAGATTTTGAAG 60.362 40.741 0.00 0.00 0.00 3.02
1933 1959 3.791320 ACTCCCACAACCTCATAGAAGA 58.209 45.455 0.00 0.00 0.00 2.87
1946 1972 2.775384 ACAGGACAACTTAACTCCCACA 59.225 45.455 0.00 0.00 0.00 4.17
1950 1976 6.371825 CCATCTTTACAGGACAACTTAACTCC 59.628 42.308 0.00 0.00 0.00 3.85
1951 1977 6.935208 ACCATCTTTACAGGACAACTTAACTC 59.065 38.462 0.00 0.00 0.00 3.01
1975 2001 3.054361 TCTTTCCTTGGGGATCTTGCTAC 60.054 47.826 0.00 0.00 41.87 3.58
2002 2028 9.753674 TTTTGTAGAACTCTCCATTTATTCCAT 57.246 29.630 0.00 0.00 0.00 3.41
2016 2042 5.739161 CCGCAATAAGCATTTTGTAGAACTC 59.261 40.000 0.00 0.00 46.13 3.01
2038 2065 2.223688 TGCTTTGTGATTTGTTCCACCG 60.224 45.455 0.00 0.00 32.61 4.94
2039 2066 3.451141 TGCTTTGTGATTTGTTCCACC 57.549 42.857 0.00 0.00 32.61 4.61
2070 2098 6.560003 TGTATCATTGTTATCAGTCCCAGT 57.440 37.500 0.00 0.00 0.00 4.00
2114 2142 3.257873 AGGTCTCAGTCTCAGATTGTGTG 59.742 47.826 0.00 0.00 0.00 3.82
2139 2167 2.761208 ACCTATTGTCTTCAGTCCTCGG 59.239 50.000 0.00 0.00 0.00 4.63
2141 2169 5.407407 TTGACCTATTGTCTTCAGTCCTC 57.593 43.478 0.00 0.00 44.75 3.71
2148 2176 6.417930 GTGCTTTTGTTTGACCTATTGTCTTC 59.582 38.462 0.00 0.00 44.75 2.87
2204 2232 3.572682 CCTGTTTTTCCAAAGTAGGGTCC 59.427 47.826 0.00 0.00 0.00 4.46
2229 2257 0.810823 TGCTGCAAAAAGGCAAGCAC 60.811 50.000 0.00 0.00 44.40 4.40
2261 3178 0.178981 CCACCCCTTCATATGGGCAG 60.179 60.000 2.13 0.00 46.43 4.85
2269 3186 1.381867 TGGATGTTCCACCCCTTCAT 58.618 50.000 0.00 0.00 42.67 2.57
2300 3217 5.658474 TGGATGGATGGAGAGATCTGAATA 58.342 41.667 0.00 0.00 0.00 1.75
2302 3219 3.902467 CTGGATGGATGGAGAGATCTGAA 59.098 47.826 0.00 0.00 0.00 3.02
2307 3224 1.360185 GCCTGGATGGATGGAGAGAT 58.640 55.000 0.00 0.00 38.35 2.75
2310 3239 0.765903 GAGGCCTGGATGGATGGAGA 60.766 60.000 12.00 0.00 38.35 3.71
2315 3244 0.327867 TCCTTGAGGCCTGGATGGAT 60.328 55.000 12.00 0.00 38.35 3.41
2319 3248 1.433121 GATCTCCTTGAGGCCTGGAT 58.567 55.000 12.00 3.74 34.44 3.41
2339 3268 8.618702 ATTCTGCCACTATCTTATCAATCTTG 57.381 34.615 0.00 0.00 0.00 3.02
2348 3277 9.533831 TCAGACATATATTCTGCCACTATCTTA 57.466 33.333 14.88 0.00 40.39 2.10
2360 3289 7.687388 AGCATTGGTCATCAGACATATATTCT 58.313 34.615 0.00 0.00 46.80 2.40
2365 3294 6.269538 AGAGTAGCATTGGTCATCAGACATAT 59.730 38.462 0.00 0.00 46.80 1.78
2396 3325 3.776969 AGTCAGCCATCTCCATTTCACTA 59.223 43.478 0.00 0.00 0.00 2.74
2399 3328 3.349927 CAAGTCAGCCATCTCCATTTCA 58.650 45.455 0.00 0.00 0.00 2.69
2409 3338 2.026542 TCTCTTGATGCAAGTCAGCCAT 60.027 45.455 7.02 0.00 41.66 4.40
2417 3346 3.468770 CTCCTCCATCTCTTGATGCAAG 58.531 50.000 0.00 0.84 46.43 4.01
2418 3347 2.172082 CCTCCTCCATCTCTTGATGCAA 59.828 50.000 0.00 0.00 46.43 4.08
2444 3394 0.325933 CATCTTGCTCCTGGGTGTCA 59.674 55.000 0.00 0.00 0.00 3.58
2461 3411 3.708631 AGGCTCTACTGATGCTACAACAT 59.291 43.478 0.00 0.00 0.00 2.71
2476 3426 6.424032 TCATAAGTGTCACTTAGAGGCTCTA 58.576 40.000 25.46 20.11 43.17 2.43
2516 3466 5.483685 TGTTAGCAACTGTCTTGGATAGT 57.516 39.130 0.00 0.00 35.60 2.12
2535 3485 5.827797 TCCACTTCTATTTCTGTTGCTTGTT 59.172 36.000 0.00 0.00 0.00 2.83
2559 3509 0.326264 CTGGTAGCTTGAACTGGCCT 59.674 55.000 3.32 0.00 0.00 5.19
2565 3515 1.266989 GTTGTGCCTGGTAGCTTGAAC 59.733 52.381 0.00 0.00 0.00 3.18
2597 3547 2.632512 CACCATAGTTTTGCCAAAGGGT 59.367 45.455 0.00 0.00 36.17 4.34
2602 3552 3.517296 TCTCCACCATAGTTTTGCCAA 57.483 42.857 0.00 0.00 0.00 4.52
2616 3566 5.860716 GCTTGAATTCTTGTGATTTCTCCAC 59.139 40.000 7.05 0.00 35.07 4.02
2625 3575 5.833406 TTCACTTGCTTGAATTCTTGTGA 57.167 34.783 7.05 8.75 30.29 3.58
2634 3584 8.203485 ACTTTCCAAATATTTCACTTGCTTGAA 58.797 29.630 0.00 0.00 33.55 2.69
2649 3599 7.169982 CGTACCAATTTTTGCACTTTCCAAATA 59.830 33.333 0.00 0.00 32.76 1.40
2674 3624 3.302365 AGGAAAATGCATGTTGGTTCG 57.698 42.857 6.90 0.00 0.00 3.95
2683 3633 6.658816 GGGGTTATTGAAAAAGGAAAATGCAT 59.341 34.615 0.00 0.00 0.00 3.96
2685 3635 6.237901 AGGGGTTATTGAAAAAGGAAAATGC 58.762 36.000 0.00 0.00 0.00 3.56
2687 3637 6.792473 AGGAGGGGTTATTGAAAAAGGAAAAT 59.208 34.615 0.00 0.00 0.00 1.82
2694 3644 8.728596 TCAATAAAGGAGGGGTTATTGAAAAA 57.271 30.769 13.64 0.00 46.27 1.94
2729 3682 8.836413 TGTTCGTCAATATCCATTCCTATTTTC 58.164 33.333 0.00 0.00 0.00 2.29
2739 3692 8.178313 TGACTACTATGTTCGTCAATATCCAT 57.822 34.615 0.00 0.00 33.84 3.41
2750 3703 5.998981 ACTAGGAGGATGACTACTATGTTCG 59.001 44.000 0.00 0.00 41.81 3.95
2764 3722 5.402054 AGATCTCAAGTGACTAGGAGGAT 57.598 43.478 12.44 6.60 0.00 3.24
2766 3724 5.530915 CAGTAGATCTCAAGTGACTAGGAGG 59.469 48.000 0.00 0.00 0.00 4.30
2799 3757 3.629142 ACATTAACCAGCTAGGGTGTC 57.371 47.619 0.00 0.00 41.32 3.67
2822 3780 9.599866 CACATATTCTCATAAACCAGTTCTACA 57.400 33.333 0.00 0.00 0.00 2.74
2931 3889 0.828022 TAGTCATAGGCCACAACCCG 59.172 55.000 5.01 0.00 0.00 5.28
2944 3902 2.903784 TGCTTGCCCCGTATATAGTCAT 59.096 45.455 0.00 0.00 0.00 3.06
2997 3955 3.959535 TGCCCCTCACATTTCAAAATC 57.040 42.857 0.00 0.00 0.00 2.17
2998 3956 3.620472 GCATGCCCCTCACATTTCAAAAT 60.620 43.478 6.36 0.00 0.00 1.82
3004 3962 0.974010 CTGGCATGCCCCTCACATTT 60.974 55.000 33.44 0.00 34.56 2.32
3054 4012 6.463995 TGGATGGTTTTATCTTACCAATGC 57.536 37.500 0.00 0.00 46.74 3.56
3056 4014 8.608185 ACAATGGATGGTTTTATCTTACCAAT 57.392 30.769 0.00 0.00 46.74 3.16
3067 4025 7.507616 TCTTGTAAACCTACAATGGATGGTTTT 59.492 33.333 18.73 8.44 46.72 2.43
3073 4031 7.259088 AGTCTCTTGTAAACCTACAATGGAT 57.741 36.000 0.00 0.00 44.95 3.41
3085 4043 7.507733 ACTCTCTTTCGTAGTCTCTTGTAAA 57.492 36.000 0.00 0.00 0.00 2.01
3099 4057 2.659279 GAGTCGCAGAAACTCTCTTTCG 59.341 50.000 0.00 0.00 39.69 3.46
3114 4072 5.123979 ACCAAGAATTTCATAAAGGAGTCGC 59.876 40.000 0.00 0.00 0.00 5.19
3115 4073 6.743575 ACCAAGAATTTCATAAAGGAGTCG 57.256 37.500 0.00 0.00 0.00 4.18
3125 4083 7.004086 TGTCTTCCACTAACCAAGAATTTCAT 58.996 34.615 0.00 0.00 0.00 2.57
3132 4090 5.009610 GCAAAATGTCTTCCACTAACCAAGA 59.990 40.000 0.00 0.00 0.00 3.02
3149 4107 4.382345 GAAGGAGATTCCAGGCAAAATG 57.618 45.455 0.00 0.00 39.61 2.32
3174 4132 2.010145 GCGTCTAGCTGAACCAATGA 57.990 50.000 0.00 0.00 44.04 2.57
3188 4146 1.204941 GACACCTACCAAGATGCGTCT 59.795 52.381 1.48 1.48 35.82 4.18
3191 4149 0.172578 TCGACACCTACCAAGATGCG 59.827 55.000 0.00 0.00 0.00 4.73
3193 4151 4.822350 TCTAGATCGACACCTACCAAGATG 59.178 45.833 0.00 0.00 0.00 2.90
3197 4155 5.050126 AGATCTAGATCGACACCTACCAA 57.950 43.478 23.77 0.00 42.48 3.67
3200 4158 8.325421 TCATAAAGATCTAGATCGACACCTAC 57.675 38.462 23.77 1.08 42.48 3.18
3222 4181 7.633789 AGTAATGGTCCAGTCTAAAACATCAT 58.366 34.615 0.00 0.00 0.00 2.45
3255 4214 9.787435 TTTTTAACCTAACAGTACATGAGACAT 57.213 29.630 0.00 0.00 0.00 3.06
3257 4216 9.269453 ACTTTTTAACCTAACAGTACATGAGAC 57.731 33.333 0.00 0.00 0.00 3.36
3439 4400 6.493115 CCATCTATGGTTAACATGCCCATTAA 59.507 38.462 8.10 0.00 43.05 1.40
3531 4493 9.936329 ATTTGACTGGTTATTATCCCAAGTAAT 57.064 29.630 0.00 0.00 0.00 1.89
3559 4521 8.948401 AAGTCTATGTATGGTAGAGATGATGT 57.052 34.615 0.00 0.00 0.00 3.06
3593 4555 6.948589 AGGGAAAAACTTATCTAGGTCAGTC 58.051 40.000 0.00 0.00 0.00 3.51
3600 4562 5.952347 AGGCCAAAGGGAAAAACTTATCTAG 59.048 40.000 5.01 0.00 35.59 2.43
3645 4607 2.094762 GGTGTGTGATCACTACCCAC 57.905 55.000 28.21 24.25 44.14 4.61
3667 4629 3.146104 ACAAACCTGAATCCCAGACAG 57.854 47.619 0.00 0.00 45.78 3.51
3685 4647 8.426569 ACTACTAGACTTGGGTTGTTTATACA 57.573 34.615 0.00 0.00 0.00 2.29
3734 4696 5.443230 AGGTTTGGAAATCCTCTCTAAGG 57.557 43.478 0.44 0.00 42.21 2.69
3735 4697 7.625469 ACTAAGGTTTGGAAATCCTCTCTAAG 58.375 38.462 0.44 0.00 45.03 2.18
3736 4698 7.569599 ACTAAGGTTTGGAAATCCTCTCTAA 57.430 36.000 0.44 0.00 45.03 2.10
3737 4699 7.569599 AACTAAGGTTTGGAAATCCTCTCTA 57.430 36.000 0.44 0.00 45.03 2.43
3738 4700 6.455690 AACTAAGGTTTGGAAATCCTCTCT 57.544 37.500 0.44 0.00 45.03 3.10
3739 4701 8.101419 TCTTAACTAAGGTTTGGAAATCCTCTC 58.899 37.037 0.44 0.00 45.03 3.20
3740 4702 7.985589 TCTTAACTAAGGTTTGGAAATCCTCT 58.014 34.615 0.44 0.00 45.03 3.69
3741 4703 8.631480 TTCTTAACTAAGGTTTGGAAATCCTC 57.369 34.615 0.44 0.00 45.03 3.71
3743 4705 8.631480 TCTTCTTAACTAAGGTTTGGAAATCC 57.369 34.615 0.00 0.00 36.92 3.01
3762 4724 7.624549 TGAGTAGGAGCATTACAATTCTTCTT 58.375 34.615 0.00 0.00 0.00 2.52
3773 4735 5.191722 AGTTTTCCCATGAGTAGGAGCATTA 59.808 40.000 0.00 0.00 32.57 1.90
3845 4807 7.342581 TCATTGTTGCTACTCCACCATTTATA 58.657 34.615 0.00 0.00 0.00 0.98
3846 4808 6.186957 TCATTGTTGCTACTCCACCATTTAT 58.813 36.000 0.00 0.00 0.00 1.40
3851 4813 2.290260 CCTCATTGTTGCTACTCCACCA 60.290 50.000 0.00 0.00 0.00 4.17
3867 4829 4.292186 TGCTTTCTAAGTTCAGCCTCAT 57.708 40.909 0.00 0.00 0.00 2.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.